See pages 316 and 364 of Deathly Hallows for mention of the Taboo. I'm referencing the British hardcovers, but they're in the chapters Xenophilius Lovegood and Malfoy Manor respectively.
It's not clear in canon if the incident with Kingsley was all it took for the Order to figure out that Voldemort's name was Taboo. There were very few people willing to say 'Voldemort' at all, except for those who were serious about standing up to him, i.e. the Order. I don't think it would have taken them long to figure out that Voldemort's named was Tabooed. ETA: In the beginning of the chapter The Bribe in DH, the trio and Lupin discuss how the trio was found so quickly at Tottenham Court, and that does send up red flags for Lupin.
Fenrir Greyback references that they have managed to track several Order members via the Taboo.
ETA: Okay, I've both thought about this and done some poking around online. I think that there is often so much focus on Hermione's intellectualism and superior intelligence that people forget she is a Gryffindor, one of the brave at heart. Hermione, in particular, throughout the series, struggled with saying 'Voldemort' openly; she worked hard at overcoming this emotional handicap because, I believe, she was wholly invested in Dumbledore's encouragement to not set fear in a name, for it would only serve to increase irrational fear of the thing itself. Dumbledore, the series' patriarch, is vehement and steadfast in his reproachment of Tom Riddle and Riddle's ridiculousness with the whole over-the-top 'Lord Voldemort' moniker. But the thing is, people totally bought into it! Voldemort's fear ploy works, to the point where the Wizarding world is debilitated.
Anyhow, I think it would have been a huge source of personal pride for Hermione when she was able to finally overcome her innate fear of saying 'Voldemort.' She stepped up to Harry's and Dumbledore's level of bravery and their commitment to refusing to be manipulated by an an overwrought superstition. The Order members took the same stance. I think that perhaps Hermione's pride and sense of accomplishment in overcoming her fear of saying 'Voldemort' may have supplanted her ability to immediately hone in on the connection between saying the name and the Death Eaters appearing. Remember, she has spent an inordinate amount of time overcoming the idea that nothing bad will happen by saying 'Voldemort.' Yes, Hermione is brilliant, but no-one is infallible, and there's a reason why Hermione was placed in Gryffindor rather than Ravenclaw.
This is my interpretation, but some similar points are made HERE in Broken Wand: How J.K. Rowling Killed Harry Potter by Timothy Wolf, a book which seems to take Rowling to task for apparent canon discrepancies. This is not what I would call a canon source, obviously, but you try Googling "JK Rowling Hermione Taboo" and see what you find ;) Hem Hem. . .